The Human Microbiome - Online Tutor, Practice Problems & Exam Prep

The human microbiome, comprising resident and transient microbiota, plays a crucial role in health. Resident microbiota are long-term inhabitants, while transient microbiota are temporary, often including pathogens. The Human Microbiome Project aims to understand microbiome composition and its health impacts, revealing that factors like birth method and diet influence microbiome development. A balanced microbiome supports immune tolerance, preventing autoimmune diseases, while dysbiosis can lead to health issues. Additionally, the microbiome aids digestion by producing essential vitamins and enzymes, highlighting its importance in nutrient synthesis and overall well-being.

The Human Microbiome

In this video, we're going to refocus our attention on the human microbiome. And so first, we need to recall from some of our previous lesson videos is that the microbiome is also sometimes referred to as normal flora. And so the microbiome or the normal flora refers to the communities of microbes that grow on and in the bodies of all humans at all times. And so these microbes that are part of the microbiome or normal flora live in symbiotic relationships with humans, and they can be further classified into 2 groups. They can be classified as resident microbiota or they could be classified as transient microbiota. Now resident microbiota, as its name implies, include microbes that are going to be residing in our bodies for long periods of time. And so the resident microbiota are microbes that are almost always on or in the host for extended long periods of time. Now the transient microbiota on the other hand, as its name implies, includes microbes that are only temporarily found on the body for relatively short periods of time. And so, of course, pathogens, disease-causing agents, are going to be considered transient microbiota. They're only on us for relatively short periods of time in most cases, but not in all cases. Now if we take a look at our image down below, we can get a better understanding of the difference between resident and transient microbiota. And so if we take a look at the left-hand side over here, notice it's an image focused on the resident microbiota, which, of course, are going to be microbes that are almost always on the host for extended periods of time. And so notice here we have a cartoon showing you these microbes that are residing in the lungs calling the lungs home sweet home. And notice it's saying, I love our home in the lungs. I never want to leave. And they seem pretty comfortable and relaxed and they don't look like they're going anywhere anytime soon. And so these resident microbiota are on or in our bodies for long periods of time. Now on the right-hand side, we're focused on the transient microbiota. And the transient microbiota, of course, are only found in our bodies for temporary periods of time or short periods of time. And so notice that these microbes right here don't look like they're sticking around much longer. They've got their bags packed and they're ready to hop on the microbe transit to make their way to their next destination because they're not going to remain in or on the host for extended periods of time. So notice their next stop is going to be outside of the host, and again, they are going to be temporarily found on the body. And so this here concludes our brief intro to the microbiome and normal flora and our, intro to resident and transient microbiota, and we're going to continue to talk more about the microbiota as we move forward in our course. So I'll see you all in our next video.

Scientists commonly call humans 'superorganisms'. What is this description referring to?

a) Humans are the most intelligent and influential organisms on the planet.

b) Each human is an ecosystem for trillions of microorganisms.

c) Humans are the only organisms that determine the success of other organism species.

d) Each human is host to a unique species of microorganism.

• A. Humans are the most intelligent and influential organisms on the planet.
• B. Each human is an ecosystem for trillions of microorganisms.
• C. Humans are the only organisms that determine the success of other organism species.
• D. Each human is host to a unique species of microorganism.

Which of the following answers does not include an example of transient microbiota?

• A. Microorganisms that inhabit certain body sites for extended periods of time.
• B. Microorganisms that are able to inhabit different body sites during their lifetime.
• C. Microorganisms that only occupy the body for a short period of time.
• D. Microorganisms that are pathogenic and eventually removed by the body's immune system.

Microbiome Composition

In this video, we're going to discuss the composition of the human microbiome. It turns out that in 2007, the Human Microbiome Project started. The Human Microbiome Project is really just a set of coordinated studies that are all designed to reveal the composition of the human microbiome. It also aims to study the relationships of the normal flora or the microbiome with various human hosts. One of the main goals of the Human Microbiome Project is to understand how changes in the microbiome throughout a person's lifetime can affect that person's health and disease. It's important to note that humans actually start to develop their microbiomes at birth, and it turns out that even the birthing method can affect the microbiome. Infants that experience a vaginal birth will be exposed to different microbes than infants that are born through a cesarean birth. Also, breast milk actually contains many beneficial microbes and carbohydrates that are really important for an infant's microbiome. The feeding method and the diet can also contribute to the microbiome.

Now in adults, there are many, many different factors that contribute to the microbiome changes that occur over a person's lifetime. Below in this image, we are showing you many of the different factors that can contribute to the microbiome. Interestingly, the microbiomes of obese adults actually differ from the microbiomes of lean adults. This goes to show that the microbiome can impact things such as obesity. Over time, it's important to note that a person's microbiome can change, and the person's microbiome changes as they are exposed to or encounter new microbes and new environments. A person's microbiome today may be different than their microbiome a year from now depending on their experiences and the microbes and environments they were exposed to.

Interestingly, researchers have begun to find a correlation between the microbiome composition and disease. It turns out that having an unhealthy microbiome can lead to a higher risk of disease. For example, intestinal dysbiosis, which refers to an imbalance of the microbiome, can actually lead to inflammatory bowel disease. By not having an appropriate intestinal microbiome, it could lead to an increased risk of inflammatory bowel disease. Taking a look at our image again, we can see many of the different factors that contribute to the microbiome. Again, humans acquire their microbiome at birth, and again the birthing method can affect the microbiome, the feeding method in terms of breast milk or formula, whether the baby goes to a daycare or a public school, or if they are homeschooled, they can be exposed to different microbes in different environments. Genetics can also play a part in the microbiome. Whether you have siblings can change the environment and again change the microbes that a person is exposed to. Different types of infections can also affect the microbiome and make changes in the microbiome. The diet that a person has throughout their lifetime, whether they are eating healthy foods or more fatty foods, will affect the type of microbiome that they have. Medications and vaccinations that a person may receive could affect their microbiome. The particular season, so in the summertime and the wintertime, a person's microbiome could change or differ, and habits such as smoking can also impact a person's microbiome, including secondhand smoking as well for infants.

All of these different factors can contribute to a person either having a healthy microbiome, a balanced microbiome that is appropriate, or it could lead to dysbiosis, which recall that dysbiosis once again is an imbalance in the microbiome. Notice here there is a lot more of this microbe and much less of this microbe, and that creates this imbalance, and the imbalance, this dysbiosis can lead to an increased risk of disease. For example, as said earlier, intestinal dysbiosis could lead to inflammatory bowel disease, and notice that this person here is not feeling well because their microbiome is not balanced. This concludes our brief lesson on microbiome composition, and we'll be able to get some practice applying these concepts as we move forward in our course and learn more about the microbiome as well. I'll see you all in our next video.

Which of the following influences the types and amounts of microorganisms found in and on your body?

• A. Your age.
• B. Your diet.
• C. Your medications.
• D. All of the above.

Recent research suggests that babies born via cesarean section are more at risk for developing allergies. Why might this be?

• A. C-sections babies are not exposed to the mother's vaginal microbiota.
• B. Early exposure to normal microorganisms of the microbiome will allow a baby's microbiome to form quicker.
• C. A less developed microbiome causes an individual to be more sensitive and reactive to allergens.
• D. All of the above.

Newborn babies acquire the microbes of their microbiota by:

• A. Passing through the birth canal.
• B. Breastfeeding.
• C. Contact with their mother's skin.
• D. Their environment.
• E. All of the above are a source of microbiota.

Microbiome Protects Against Infection

In this video, we're going to discuss how the human microbiome can protect against infection. First, we need to recall from some of our previous lesson videos that the microbiome itself is actually part of innate immunity because it can protect against pathogens nonspecifically. This is because the microbiome can create a competitive and unfavorable environment for pathogens, protecting us from them. Some of the microbes in our microbiome can block the attachment sites that pathogenic microbes need to use to colonize the area. By blocking these attachment sites, the microbes of the microbiome are preventing pathogenic microbes from infecting us. Other microbes of the microbiome can also create toxins or toxic substances that are not toxic to us, but they are only going to be harmful and toxic to some pathogenic microbes, again protecting us from those pathogenic microbes.

If we take a look at our first image down below, notice that it's focused on how the microbiome can protect against infection. On the left, we are showing you a human, and you can see all of the different microbes that are part of the microbiota on this human. Just outside of the human, there are some pathogenic microbes. If we zoom into this particular region, you'll notice that within the human, we have the normal microbiota, and on the outside of the human, we have the pathogenic microbes. In this cartoon, the normal microbiota is saying "you are not welcome here" to the pathogenic microbes. The pathogenic microbes are saying, "hey, they're blocking all of the attachment sites." These pathogenic microbes are not going to be able to colonize the human body because of the normal microbiota blocking the attachment sites and creating toxins that prevent the pathogenic microbes from infecting us.

Another thing that our microbiome can do is it can actually stimulate the adaptive immune system towards pathogens that we have not even yet encountered. Imagine a situation where a small number of skin microbiota actually enter into our tissues via cuts that might be in our skin. When these small numbers of skin microbiota enter into our tissues via cuts, our body and our immune system can actually produce antibodies against the skin microbiota. These antibodies that were produced against the skin microbiota can also be effective against pathogens that have similar antigens to the skin microbiota, ultimately protecting us against pathogens that we have not even yet encountered.

Looking at our second image down below, we get a better understanding of how the microbiome can actually stimulate the adaptive immune system. In this image, we have a cartoon with two scenes. The left scene represents the human body, specifically the skin, where we have a wound site with an open wound. Skin microbiota, normal and healthy on our skin, can make their way into the tissues via the wound site. One of the skin microbiota cells, curious, makes its way into the tissues and our adaptive immune system, such as our B cells, recognize them, saying "you shouldn't be here," and they start to create antibodies towards the skin microbiota. In the next scene, the skin microbiota, a little beat up from going in the first time, warns a pathogen that looks similar in terms of surface antigens, saying "if you go in there, it's over". The pathogen, undeterred, goes into the tissues and realizes it has made a mistake because there are already antibodies that are effective against him.

This concludes our brief lesson on how the microbiome can protect against infection and pathogens, and we'll be able to get some practice applying these concepts as we move forward and learn more as well. So I'll see you guys in our next video.

Which of the following is not a way in which our microbiome helps protect our bodies from pathogens?

• A. Microbes of our microbiome create compounds that helps us digest our food.
• B. Microbes of our microbiome create compounds that are harmful to pathogenic microbes.
• C. Microbes of our microbiome outcompete pathogenic microbes for resources.
• D. Microbes of our microbiome block entrances and binding sites in our bodies.

Certain antibiotics inhibit the growth of Lactobacillus species of bacteria. Adult women who take these antibiotics commonly have vaginal yeast infections following their antibiotic treatments. . Which of the following statements about the Lactobacillus bacteria and yeast of the vagina is false?

• A. The yeast is a pathogenic microbe in the vagina.
• B. The Lactobacillus bacteria and yeast compete for resources in the healthy microbiome.
• C. The antibiotics have caused an imbalance of the bacterial and yeast populations of the vagina.

Microbiome Promotes Immune Tolerance

In this video, we're going to talk about how the human microbiome can actually promote immune tolerance. Now before we continue, it's important to recall from some of our previous lesson videos that we've already discussed immune tolerance. And so, if you don't remember much about immune tolerance, be sure to go back and check out those videos before you continue here. Now that being said, it's important to note that both T and B cells must be able to build immune tolerance to our microbiome or towards our normal flora in order for the T and B cells to avoid attacking our microbiome. And so, again, recall from some of our previous lesson videos that immune tolerance can be defined as the ability for our immune system to distinguish between harmless antigens and harmful antigens. And immune tolerance is very important for preventing autoimmunity or autoimmune diseases, which are characterized by our immune system attacking our own healthy cells.

Now also recall from some of our previous lesson videos that regulatory T cells or Treg cells are important for preventing autoimmunity as well. And that's because these regulatory T cells or Treg cells are going to inhibit the activity of other T cells and prevent those other T cells from targeting the host's microbiome and healthy cells, which, again, we do not want our immune system targeting these cells. Now interestingly enough, it turns out that there are many scientific studies that have shown that early and sufficient exposure to microbes as an infant or child can actually help to increase Treg cell activity or regulatory T cell activity. And that, again, is going to help prevent autoimmune diseases and, can also help to prevent allergies as well.

This directly leads us into what is known as the hygiene hypothesis, which basically states that insufficient exposure to microbes can actually increase a person's risk of developing allergies and autoimmune disorders. And so if we take a look at our image down below, we can get a better understanding of both the hygiene hypothesis and how the microbiome can help to promote immune tolerance. And so notice that this image is broken up into a top half here with a yellow background, and the bottom half here with a pinkish background. And what you'll notice is that on the far left over here, we're showing you an infant or a child here who has exposure to many microbes as an infant. So you can see the diversity of microbes that this infant is exposed to. And, being exposed to so many different microbes at a young age can help to create high regulatory T cell activity. And so notice that there are many regulatory T cells with high activity. And, again, recall that the regulatory T cells like this cartoon is trying to display, they are important for inhibiting the activity of other immune cells to prevent them from attacking the healthy microbiome and healthy cells. And so notice over here, we're showing you these immune system cells that are looking to destroy the microbes. However, the regulatory T cell says stop, only destroy the pathogens. And so it's preventing an immune response towards the healthy microbiome, and helping to redirect the immune cells to target the pathogens only. And so with high Treg cell activity, the immune system is able to build a tolerance for the microbiome. Tolerating the microbiome so that it is not targeted and only attacking the dangerous pathogens.

Now on the bottom left over here, we're showing you an infant or baby that is having exposure to, few very few microbes as an infant. So notice that here we only have very few microbes in comparison to all of these microbes the top baby is exposed to. And so having very few microbe exposure as an infant or child will lead to relatively low regulatory T cell activity or Treg activity. And so notice here that we have a relatively low number of these Treg cells. And so under these conditions, the immune system is going to be at a higher risk of lacking tolerance towards the microbiome. And so that can lead to increased risk of allergies as well as increased risk of autoimmune disorders. And so once again, notice in this cartoon, we're showing you the immune system cells looking to target these microbes. And notice that with low regulatory T cell activity, it will not be able to inhibit these immune cells in the way that they should. And so, notice here that the Treg is saying I can't tell the difference between them anyways, but ultimately it's just that these Treg cell these, immune system cells here will be targeting both the healthy microbiome as well as the pathogens. And again, that could lead to potential allergies and autoimmune disorders.

And so this here concludes our brief lesson on the microbiome and how it can promote immune tolerance. And we also discussed a little bit about the hygiene hypothesis here. And so we'll be able to get some practice applying these concepts as we move forward in our course. So I'll see you all in our next video.

The "hygiene hypothesis"proposes that during childhood:

• A. Lack of exposure to microbes can promote development of allergies.
• B. Hand washing prevents against most dangerous infections.
• C. The immune system develops best in a clean environment.

Microbiome Makes Nutrients & Aids in Host Digestion

In this video, we're going to talk about how members of our normal microbiome can actually make nutrients for the host and aid in host digestion as well. And so once again, an important feature of the microbiome is its ability to produce essential nutrients for the host. And so down below, we have three examples of how the microbiome can either make nutrients for the host or aid in host digestion. And so intestinal microbiome members can actually produce essential vitamins that are critical for the host. For example, vitamins B and vitamin K that can be absorbed and utilized by the host. Also, intestinal microbiome members can also produce enzymes that are capable of degrading complex carbohydrates for the host, essentially aiding in host digestion, helping the host break down complex carbohydrates so that the host can utilize the smaller segments of those carbohydrates. And then last but not least here, we're also mentioning how fermenting bacteria that are part of the normal microbiome can also produce energy sources for epithelial cells.

And so if we take a look at our image down below, we can get a better understanding of how the microbiome can, once again, make nutrients for the host and aid in digestion. And so notice over here we're showing you a human, and we're zooming in specifically to the gut region here. And, within the gut, you can see that there are going to be many microbiome, many microbes that are part of the microbiome. And so the microbes of the large and small intestine here, which you'll notice, here we have these blue microbes that are producing vitamin B, and here this microbe is producing vitamin K. And so, we can label this as vitamins that are being produced by members of the microbiome. And then, of course, the host can utilize these essential critical vitamins for its own use. Down below over here in the bottom left of our image, we're showing you how some of the members of the microbiome can actually produce enzymes, represented here as these little tiny scissors. And these enzymes are capable of degrading complex carbohydrates into smaller components, and that is going to aid in digestion. And so these enzymes can degrade these complex carbohydrates for the host. And then last but not least here, we're also showing you some fermenting bacteria here that are capable of producing energy sources that can be utilized by epithelial cells allowing them to obtain energy.

And so ultimately, the big takeaway here is that the normal microbiome plays a critical role in making nutrients for the host and aiding in host digestion. And once again, without the members of the normal microbiome, life as we know would not be able to exist. And so we rely on our microbiome to create nutrients and to aid in our digestion. And so this here concludes our brief lesson on this, and we'll be able to get some practice applying this as we move forward. So I'll see you all in our next video.

Which of the following is true about how the microbes of our microbiome help maintain our health?

• A. They block pathogen attachment to host cells.
• B. They establish competition for available nutrients and vitamins.
• C. They produce antimicrobial substances that damage pathogenic microbes.
• D. They stimulate the immune system to attack pathogenic microbes.
• E. All of the choices are true.

Humans do not possess the enzymes required to break down most dietary fibers found in whole grains, beans, and vegetables. However, some fiber can be digested in our guts. How does this happen?

• A. Certain bacteria in our gut microbiome digest the fiber in our food and provide us with nutrients.
• B. Certain yeasts in our gut create vitamins which help break down fiber in our food.
• C. Certain bacteria in our gut induce our intestinal epithelial cells to create enzymes which can break down fiber.

Here’s what students ask on this topic:

What is the human microbiome and why is it important?

The human microbiome, also known as the normal flora, refers to the communities of microbes that reside on and within the human body. These microbes live in symbiotic relationships with humans and can be classified into resident microbiota, which are long-term inhabitants, and transient microbiota, which are temporary. The microbiome is crucial for several reasons: it aids in digestion by producing essential vitamins and enzymes, supports immune tolerance to prevent autoimmune diseases, and protects against infections by creating an unfavorable environment for pathogens. A balanced microbiome is essential for overall health, while an imbalance, known as dysbiosis, can lead to various health issues.

How does the Human Microbiome Project contribute to our understanding of health and disease?

The Human Microbiome Project, initiated in 2007, is a set of coordinated studies aimed at revealing the composition of the human microbiome and understanding its relationship with human health and disease. One of its main goals is to determine how changes in the microbiome throughout a person's lifetime can affect their health. The project has shown that factors like birth method, diet, and environment influence microbiome development. It has also found correlations between microbiome composition and diseases, such as how an unhealthy microbiome can increase the risk of conditions like inflammatory bowel disease. This research is crucial for developing new treatments and preventive measures for various health issues.

How does the human microbiome protect against infections?

The human microbiome protects against infections as part of innate immunity by creating a competitive and unfavorable environment for pathogens. Microbes in the microbiome can block attachment sites that pathogens need to colonize, preventing infections. Additionally, some microbiome microbes produce toxins that are harmful to pathogens but not to humans. The microbiome can also stimulate the adaptive immune system by producing antibodies against similar antigens, providing protection against pathogens not yet encountered. This dual role in both innate and adaptive immunity highlights the microbiome's importance in maintaining health and preventing infections.

What factors influence the composition of the human microbiome?

Several factors influence the composition of the human microbiome, starting from birth. The birthing method (vaginal vs. caesarean) and feeding method (breast milk vs. formula) significantly impact an infant's microbiome. As individuals grow, their microbiome is affected by diet, environment, genetics, infections, medications, and lifestyle habits like smoking. Seasonal changes can also alter the microbiome. These factors contribute to the dynamic nature of the microbiome, which can change over time based on new microbial exposures and environmental interactions. Understanding these influences is crucial for maintaining a balanced and healthy microbiome.

How does the microbiome aid in digestion and nutrient synthesis?

The microbiome plays a vital role in digestion and nutrient synthesis. Intestinal microbiome members produce essential vitamins, such as vitamins B and K, which are critical for the host. They also produce enzymes that degrade complex carbohydrates, aiding in digestion by breaking them down into smaller, absorbable components. Additionally, fermenting bacteria in the microbiome produce energy sources for epithelial cells. These functions highlight the microbiome's importance in nutrient synthesis and overall digestive health, emphasizing that life as we know it relies on these microbial communities for essential nutrients and efficient digestion.